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- PDB-2we9: Crystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv -

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Basic information

Entry
Database: PDB / ID: 2we9
TitleCrystal structure of Rv0371c from Mycobacterium tuberculosis H37Rv
ComponentsMOBA-RELATED PROTEIN
KeywordsUNKNOWN FUNCTION / MYCOBACTERIUM TUBERCULOSIS H37RV
Function / homology
Function and homology information


nucleotidyltransferase activity / metal ion binding
Similarity search - Function
MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
MobA-like NTP transferase domain-containing protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of Rv0371C from Mycobacterium Tuberculosis H37Rv
Authors: Cho, H.J. / Kang, B.S.
History
DepositionMar 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOBA-RELATED PROTEIN
B: MOBA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7523
Polymers42,6602
Non-polymers921
Water2,396133
1
A: MOBA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4222
Polymers21,3301
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MOBA-RELATED PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,3301
Polymers21,3301
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.181, 58.731, 143.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MOBA-RELATED PROTEIN


Mass: 21329.916 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) MYCOBACTERIUM TUBERCULOSIS H37RV (bacteria)
References: UniProt: O53706
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M MES PH 6.0 AND 18% PEG 4000 BY MICRO-SEEDING

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97948
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2007 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20560 / % possible obs: 95.4 % / Observed criterion σ(I): 2.1 / Redundancy: 11.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.96
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5 / % possible all: 73.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→31.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.897 / SU B: 15.396 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1025 5.2 %RANDOM
Rwork0.217 ---
obs0.221 18731 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2903 0 6 133 3042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222999
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1011.9644089
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9625391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37221.575127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.27215478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8081538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.190.21278
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21997
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.45631960
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.32753079
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.10881157
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.486111005
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 65 -
Rwork0.231 970 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.3883-0.3621-1.67080.6731.11696.3143-0.12530.10.0771-0.25460.159-0.0481-0.08740.2553-0.03370.0779-0.1250.0182-0.14390.05760.097141.829632.274735.5152
22.1960.7707-0.50911.66760.18272.1754-0.33370.1542-0.0806-0.26530.21330.02540.123-0.19560.12040.0037-0.06310.0186-0.1103-0.00070.094632.176124.40342.1524
318.35468.383914.79747.7519.841118.2232-0.40620.4368-0.41310.38470.64540.22190.52850.6537-0.2392-0.08130.12630.0660.01050.10330.071416.521823.637964.3301
41.46740.01940.61881.13140.55012.0095-0.1637-0.3511-0.02890.13140.09910.0141-0.0013-0.07680.0647-0.07090.11780.01970.03970.0420.067514.997430.176269.9281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 85
2X-RAY DIFFRACTION2A86 - 195
3X-RAY DIFFRACTION3B1 - 16
4X-RAY DIFFRACTION4B17 - 194

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